Ant Slayer

library(trajr)
library(tidyverse)
library(readxl)
library(kableExtra)
library (patchwork)
# library(lessR)

Load excel

ajay_page1 <- read_excel("./Data/velocity_5seq_20200219a.xlsx", col_names = T, 
sheet = "velocity_5seq_20200219", range = "A1:AB23")%>% 
  rename("filename" = "f-name") %>% 
  mutate(filename = str_replace(filename, ".$", "")) %>% 
  rename("contact" = Seq3...15) %>%
  mutate(firstMoveFrame = frame1 - posFile_start)
# View(ajay_page1)

ajay_page2 <- read_excel("./Data/velocity_5seq_20200219a.xlsx", sheet = "accl_sp_2020_May_07", range = "A1:N23")%>% 
  rename("filename" = 1, 
         "start_F" = `start-F`) %>% 
  mutate(filename = str_replace(filename, ".$", ""))

Matching pos files with spreadsheet

# Grab the names of all the files in the working directory as set above

all_pos <- list.files("./Data2", pattern =".pos", full.names = TRUE)

# Grabs the names of the video files from the control spreadsheet
# note the current directory only contains videos from the chronos camera
input_list <- ajay_page1 %>% 
  select("filename") %>% 
  pull()

# input_list

# creates a single object to be used as a pattern to grab the pos files that match those in the spreadsheet
pattern <- paste(input_list, sep="", collapse="|")

# list of pos files that match names in the spreadsheets
chosen_pos <- all_pos[grepl(pattern, all_pos)]

Containers

# first containers --------------------------------------------------------

# coord_files <- chosen_pos %>% 
  # str_subset(pattern = "-(\\d){2}.pos$")

coord_files <- chosen_pos %>% 
  str_subset(pattern = "(\\d|\\d_fail)\\.pos$")

# scale_files <- chosen_pos %>% 
  # str_subset(pattern = "_(\\d){2}mm.pos$")

scale_files <- chosen_pos %>% 
  str_subset(pattern = "(\\d){1,}_scale_(\\d){1,}(mm)|(\\d){1,}_fail_scale_(\\d){1,}(mm)\\.pos$")

# extract the known distances from the scale files
the_scales <- scale_files %>% 
  as.data.frame() %>% 
  rename("scaleFiles" = ".") %>% 
  mutate(scaleValues =  str_extract(scaleFiles, pattern = "_(\\d){1,2}mm")) %>% 
  mutate(scaleValues =  str_extract(string = scaleValues, pattern = "_\\d+")) %>% 
  mutate(scaleValues = str_replace(scaleValues, pattern = "_", replacement = "0.0")) %>% 
  mutate(scaleValues = as.numeric(scaleValues))

MAP-traj-derivs

derivs_list <- pmap(list(coord_files, scale_files, the_scales$scaleValues), loadSample_FromList2) %>% 
  map(TrajSmoothSG, p = 5, n = 23) %>% 
  map(TrajDerivatives) %>% 
  set_names(mylabelseq("Derivs_", 1, 22, 1))

derivs_names <- names(derivs_list)

for(i in seq_along(derivs_names)) {
  derivs_list[[i]] %>% plotSpeed()
  title(derivs_names[i])
}

Excluding trajectory 3

Exploration of the trajectory and speed change of the third high speed video showed an usual pattern. Further revision of the video showed that this was a failed attacked trigger towards an ant at a greater distance. Thus, the ant slayer spider did not attempt to tag the ant prey with silk. For this, the sequence is excluded.

trajs_list <- list(coords = coord_files, scales = scale_files, scaleValues = the_scales)
traj_03 <- loadSample_FromList(listObject = trajs_list, number = 3)
par(mfrow = c(1,2))
derivs_list$Derivs_03 %>% plotSpeed()
plot(traj_03, lwd = 1, lty = 1)

Separating distinct trajectories

The following trajectories do not fit general settings applied to the rest of the trajectories and are thus using particular settings shown below (section “Distinct ones”).

removables <- c(2, 3, 12)

derivs_list_short <- derivs_list[- removables]
derivs_names_short <- derivs_names[- removables]
# names(derivs_list_short) <- derivs_names_short

Frame indexes

# The "IndexLimitsManual" function pulls the index position of the following frames:
# last frame where speed is zero (the onset of the ant slayer attack)
# frame where the acrobatic strike reaches its maxumum speed

# default values used for the function
# IndexLimitsManual(derivs_object = derivs_list_sample$Derivs_01, startThreshold = 1e-8, thresholdFrame = 1, limit_range = 155, window_size = 35)

indexes_short <- map(derivs_list_short, IndexLimitsManual)
names(indexes_short)

##  [1] "Derivs_01" "Derivs_04" "Derivs_05" "Derivs_06" "Derivs_07" "Derivs_08"
##  [7] "Derivs_09" "Derivs_10" "Derivs_11" "Derivs_13" "Derivs_14" "Derivs_15"
## [13] "Derivs_16" "Derivs_17" "Derivs_18" "Derivs_19" "Derivs_20" "Derivs_21"
## [19] "Derivs_22"

Maxima speeds

The following plots show the speed change during the first phase of the attack (acrobatic strike) The blue vertical line marks the onset of the spiders’ attack (the spider begins moving) The red line shows where the peak speed was reached during the acrobatic strike Note this is restricted to the speeds achieved by the spiders while directing its attack to the ant prey and before dropping off from the trunk surface.

pmap(list(derivs_list_short, as.list(names(derivs_list_short)), indexes_short), 
     ~ggplot() + geom_line(aes(x= ..1$speedTimes*1000, y= ..1$speed*100)) +
       ggtitle(..2) +
       geom_vline(xintercept = ..3$`maxim(um/a)`*4, col = "red")+
       geom_vline(xintercept = c(..3$start_index)*4, col = "blue") + 
       xlab("Time (ms)") +
       ylab("Speed (cm/s)") +
       theme_bw()
)

## $Derivs_01

## 
## $Derivs_04

## 
## $Derivs_05

## 
## $Derivs_06

## 
## $Derivs_07

## 
## $Derivs_08

## 
## $Derivs_09

## 
## $Derivs_10

## 
## $Derivs_11

## 
## $Derivs_13

## 
## $Derivs_14

## 
## $Derivs_15

## 
## $Derivs_16

## 
## $Derivs_17

## 
## $Derivs_18

## 
## $Derivs_19

## 
## $Derivs_20

## 
## $Derivs_21

## 
## $Derivs_22

Distinct ones

Trajectories 02 and 12 were affected by noisy speed curves before the onset of the attack. These were adjusted and corroborated with visual inspection of the videos to make sure that the selected frame was the last one before the attack onset.

# removables <- c(2, 3, 12)

derivs_list_special <- derivs_list[removables]
derivs_names_special <- derivs_names[removables]
names(derivs_list_special) <- derivs_names_special
# str(derivs_list_special)

Derivs 02

# get index frames
indexes_derivs_02 <- IndexLimitsManual(derivs_object = derivs_list_special$Derivs_02, startThreshold = 1e-8, thresholdFrame = 19, limit_range = 155, window_size = 25)
# plot
ggplot() +
  geom_line(aes(x = derivs_list_special$Derivs_02$speedTimes*1000, y = derivs_list_special$Derivs_02$speed*100)) +
  geom_vline(xintercept = indexes_derivs_02$`maxim(um/a)`[2]*4, col = "red") +
  geom_vline(xintercept = c(indexes_derivs_02$start_index, indexes_derivs_02$end_index)*4, col = "blue") + 
  labs(title = "Derivs_02", 
       x = "Time (ms)",
       y = "Speed (cm/s)") +
  theme_minimal()

# indexes_derivs_02$`maxim(um/a)`
# indexes_derivs_02$end_index

Derivs 12

# get index frames
indexes_derivs_12 <- IndexLimitsManual(derivs_object = derivs_list_special$Derivs_12, startThreshold = 1e-8, thresholdFrame = 19, limit_range = 155, window_size = 35)

# plot
ggplot() +
  geom_line(aes(x = derivs_list_special$Derivs_12$speedTimes*1000, y = derivs_list_special$Derivs_12$speed*100)) +
  geom_vline(xintercept = indexes_derivs_12$`maxim(um/a)`*4, col = "red") +
  geom_vline(xintercept = c(indexes_derivs_12$start_index, indexes_derivs_12$end_index)*4, col = "blue") + 
  labs(title = "Derivs_12", 
       x = "Time (ms)",
       y = "Speed (cm/s)") +
  theme_minimal()

# indexes_derivs_02$`maxim(um/a)`
# indexes_derivs_02$end_index

The plot

Panel F in figure 1

The figure plots the speed change from the last frame before the acrobatic attack onset to the maximum speed reached for 17/19 inspected high speed videos. The remaining 2 (02 and 12) are added later.

# loop me up!
# colour palette
cbp1 <- c("#999999", "#E69F00", "#56B4E9", "#009E73",
          "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
# to recycle colours
cbp1_24 <- rep(cbp1, 3)

mp <- ggplot()
for(i in seq_along(derivs_list_short)) {
  
  idata <- tibble("speed" = derivs_list_short[[i]]$speed[indexes_short[[i]]$start_index:indexes_short[[i]]$`maxim(um/a)`]) %>% 
    mutate("index" = seq_along(speed)-1)
  
  mp <- mp + geom_line(data = idata, 
                       aes(x = index*4, y = speed*100), colour = cbp1_24[i]) +
    geom_point(data = idata,
               aes(x = last(index)*4, 
                   y =  last(speed*100)), 
               colour = cbp1_24[i]) +
    expand_limits(x = c(0, 160), y = c(0, 65)) +
    ylab("Speed (cm/s)") +
    xlab("Time (ms)") +
    theme_classic() +
    theme(panel.border = element_blank())
}

# the version below does not include speed for trajectories 02 and 12
# print(mp)


# mp + 
#   scale_y_continuous(expand = expansion(mult = c(0, .1))) +
#   scale_x_continuous(expand = expansion(mult = c(0, .1)))

Curves for trajectories 02 and 12 are created with the distinct settings created before to capture the correct frames of importance

# 02
derivs_02_data <- tibble("speed" = derivs_list_special$Derivs_02$speed[indexes_derivs_02$start_index:indexes_derivs_02$`maxim(um/a)`[2]]) %>% 
  mutate("index" = seq_along(speed)-1)

mp <- mp  +
geom_line(data = derivs_02_data, 
                     aes(x = index*4, y = speed*100), colour = cbp1_24[7]) +
  geom_point(data = derivs_02_data,
             aes(x = last(index)*4, 
                 y =  last(speed*100)), 
             colour = cbp1_24[7]) +
  expand_limits(x = c(0, 160), y = c(0, 65)) +
  ylab("Speed (cm/s)") +
  xlab("Time (ms)") +
  theme_bw()

# 12
derivs_12_data <- tibble("speed" = derivs_list_special$Derivs_12$speed[indexes_derivs_12$start_index:indexes_derivs_12$`maxim(um/a)`]) %>% 
  mutate("index" = seq_along(speed)-1)

mp <- mp  +
geom_line(data = derivs_12_data, 
                     aes(x = index*4, y = speed*100), colour = cbp1_24[8]) +
  geom_point(data = derivs_12_data,
             aes(x = last(index)*4, 
                 y =  last(speed*100)), 
             colour = cbp1_24[8]) +
  expand_limits(x = c(0, 160), y = c(0, 65)) +
  ylab("Speed (cm/s)") +
  xlab("Time (ms)") +
  theme_bw()

Plot included speed changes for all trajectories

print(mp)

# mp+theme(panel.border = element_blank())

Speed & duration

Max speeds for each spider and the elapsed time while going from 0 to to max.

results <- map_dfr(derivs_list_short, SpeedAndTime2)
# results %>% kbl() %>% 
#   kable_styling(full_width = F)

# rename("Max speed (cm/s)" = max_speed, 
#        "Elapsed time (ms)" = elapsed_time)

res_02 <- SpeedAndTime2(derivatives_list = derivs_list_special$Derivs_02, thresholdFrame = 19, window_size = 25, multiMax = 2)

res_12 <- SpeedAndTime2(derivatives_list = derivs_list_special$Derivs_12, thresholdFrame = 19, window_size = 35)

speeds_times <- bind_rows(results, res_02, res_12) %>% 
  mutate(camefrom = c(derivs_names_short, "Derivs_02", "Derivs_12")) 

speeds_times %>% kbl() %>% 
  kable_styling(full_width = F)

max_speed	elapsed_time	camefrom
11.57657	116	Derivs_01
29.94638	112	Derivs_04
61.83679	132	Derivs_05
19.86896	128	Derivs_06
11.17088	96	Derivs_07
21.52736	120	Derivs_08
31.64278	104	Derivs_09
33.36874	152	Derivs_10
14.53998	92	Derivs_11
29.30936	100	Derivs_13
29.20735	104	Derivs_14
15.24193	84	Derivs_15
25.19305	108	Derivs_16
33.06568	88	Derivs_17
25.37552	108	Derivs_18
23.51403	104	Derivs_19
30.45109	92	Derivs_20
22.21806	76	Derivs_21
15.98763	108	Derivs_22
24.35238	148	Derivs_02
32.73323	96	Derivs_12

speeds_times %>% 
  summarise(avgSpeed = mean(max_speed), avgTime = mean(elapsed_time))

# the median
table(speeds_times$elapsed_time)

## 
##  76  84  88  92  96 100 104 108 112 116 120 128 132 148 152 
##   1   1   1   2   2   1   3   3   1   1   1   1   1   1   1

median(speeds_times$elapsed_time) 

## [1] 104

inset <- speeds_times %>%
  ggplot() +
  geom_boxplot(aes(elapsed_time)) +
  expand_limits(x = c(0, 160)) +
  theme( panel.grid = element_blank(),
         axis.title = element_blank(),
         axis.text = element_blank(),
         # panel.background = element_blank(),
         panel.background = element_rect(fill = "transparent",colour = NA),
         plot.background = element_rect(fill = "transparent",colour = NA),
)
  
inset <- inset +
  theme(legend.position = "none",
        panel.grid = element_blank(),
        axis.title = element_blank(),
        axis.text = element_blank(),
        axis.ticks = element_blank(),
        # rect = element_rect(fill = "transparent"),
        # panel.background = element_blank(),
        )

Panel F in figure 1 including inset box plot for elapsed time during speed change

# mp+geom_vline(xintercept = 104)+geom_vline(xintercept = 152) +
# inset_element (p = inset,
# left = -0.018,
# bottom = 0.80,
# right = 1.012,
# top = 0.95, align_to = "panel")

ggp_combi <- mp + theme_classic() + 
  inset_element (p = inset,
                 left = -0.018,
                 bottom = 0.89,
                 right = 1.012,
                 top = 0.99, align_to = "panel")
ggp_combi

# ggsave(filename = "panelF.pdf", plot = ggp_combi, device = "pdf", path = "./gg_plots")

# setwd("/Users/alfonsoaceves/Downloads/Ant Slayer Speed/gg_plots")
# write_csv(speeds_times, "speeds_times.csv")

# title: "R Notebook"
# output:
#   html_document:
#     code_folding: "show"
#     toc: TRUE
#     toc_float: TRUE
#     df_print: paged
# editor_options:
#   chunk_output_type: console